<!DOCTYPE html>

<html lang="en" data-content_root="./">
  <head>
    <meta charset="utf-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />

    <title>GNPS Usage &#8212; TIMSCONVERT 2.0.0a5 documentation</title>
    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d1102ebc" />
    <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=12dfc556" />
    <script src="_static/documentation_options.js?v=683eb3c5"></script>
    <script src="_static/doctools.js?v=888ff710"></script>
    <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
    <link rel="index" title="Index" href="genindex.html" />
    <link rel="search" title="Search" href="search.html" />
    <link rel="next" title="Advanced Usage" href="advanced.html" />
    <link rel="prev" title="Local Usage" href="local.html" />
   
  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
  

  
  

  </head><body>
  

    <div class="document">
      <div class="documentwrapper">
        <div class="bodywrapper">
          

          <div class="body" role="main">
            
  <section id="gnps-usage">
<h1>GNPS Usage<a class="headerlink" href="#gnps-usage" title="Link to this heading">¶</a></h1>
<section id="using-timsconvert-on-gnps">
<h2>Using TIMSCONVERT on GNPS<a class="headerlink" href="#using-timsconvert-on-gnps" title="Link to this heading">¶</a></h2>
<p>The web version of TIMSCONVERT currently supports various data formats listed below. No installation is necessary. All
that is required is a GNPS account.</p>
<ol class="arabic simple">
<li><p>Upload your data to GNPS using the following <a class="reference external" href="https://ccms-ucsd.github.io/GNPSDocumentation/fileupload/">instructions</a>.</p></li>
<li><p>Go to the <a class="reference external" href="https://proteomics2.ucsd.edu/ProteoSAFe/index.jsp?params=%7b%22workflow%22%3A%20%22TIMSCONVERT%22%7d">TIMSCONVERT workflow page</a>.</p></li>
<li><p>Select your dataset.</p></li>
<li><p>Submit your run.</p></li>
<li><p>You will receive an email when your job has completed.</p></li>
</ol>
</section>
<section id="compatible-file-types-in-gnps-timsconvert-workflow">
<h2>Compatible File Types in GNPS TIMSCONVERT Workflow<a class="headerlink" href="#compatible-file-types-in-gnps-timsconvert-workflow" title="Link to this heading">¶</a></h2>
<table class="docutils align-default">
<thead>
<tr class="row-odd"><th class="head"><p>Acquisition Mode</p></th>
<th class="head"><p>Raw File Format</p></th>
<th class="head"><p>Converted File Format</p></th>
<th class="head"><p>Compatible?</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>LC-MS(/MS)</p></td>
<td><p>.d/BAF</p></td>
<td><p>mzML</p></td>
<td><p>No</p></td>
</tr>
<tr class="row-odd"><td><p>LC-MS(/MS)</p></td>
<td><p>.d/TSF</p></td>
<td><p>mzML</p></td>
<td><p>Yes</p></td>
</tr>
<tr class="row-even"><td><p>LC-TIMS-MS(/MS)</p></td>
<td><p>.d/TDF</p></td>
<td><p>mzML</p></td>
<td><p>Yes</p></td>
</tr>
<tr class="row-odd"><td><p>MALDI-MS(/MS) Dried Droplet</p></td>
<td><p>.d/TSF</p></td>
<td><p>mzML</p></td>
<td><p>Yes</p></td>
</tr>
<tr class="row-even"><td><p>MALDI-MS(/MS) Imaging Mass Spectrometry</p></td>
<td><p>.d/TSF</p></td>
<td><p>imzML</p></td>
<td><p>Yes</p></td>
</tr>
<tr class="row-odd"><td><p>MALDI-TIMS-MS(/MS) Dried Droplet</p></td>
<td><p>.d/TDF</p></td>
<td><p>mzML</p></td>
<td><p>Yes</p></td>
</tr>
<tr class="row-even"><td><p>MALDI-TIMS-MS(/MS) Imaging Mass Spectrometry</p></td>
<td><p>.d/TDF</p></td>
<td><p>imzML</p></td>
<td><p>Yes</p></td>
</tr>
</tbody>
</table>
</section>
</section>


          </div>
          
        </div>
      </div>
      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
        <div class="sphinxsidebarwrapper">
<h1 class="logo"><a href="index.html">TIMSCONVERT</a></h1>








<h3>Navigation</h3>
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="local.html">Local Usage</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">GNPS Usage</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#using-timsconvert-on-gnps">Using TIMSCONVERT on GNPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="#compatible-file-types-in-gnps-timsconvert-workflow">Compatible File Types in GNPS TIMSCONVERT Workflow</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="timsconvert.html">TIMSCONVERT Source Code</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Modules</a></li>
</ul>

<div class="relations">
<h3>Related Topics</h3>
<ul>
  <li><a href="index.html">Documentation overview</a><ul>
      <li>Previous: <a href="local.html" title="previous chapter">Local Usage</a></li>
      <li>Next: <a href="advanced.html" title="next chapter">Advanced Usage</a></li>
  </ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
  <h3 id="searchlabel">Quick search</h3>
    <div class="searchformwrapper">
    <form class="search" action="search.html" method="get">
      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
      <input type="submit" value="Go" />
    </form>
    </div>
</div>
<script>document.getElementById('searchbox').style.display = "block"</script>








        </div>
      </div>
      <div class="clearer"></div>
    </div>
    <div class="footer">
      &#169;2024, Gordon T. Luu.
      
      |
      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
      
      |
      <a href="_sources/gnps.rst.txt"
          rel="nofollow">Page source</a>
    </div>

    

    
  </body>
</html>